I have been using Design Premium CS5 for over a year, and have used the encoder before, but I do not remember having this issue. I can only export in FLV / FV4 and H.264. My understanding is that this is supposed to be the "trial" formats, but having purchased CS5 and having it registered it for a while, I am under the impression that it should be a "paid" version. Any ideas?

You're correct that the trial version of AME CS5 had a limited set of export (and import) formats. However, when the point product or suite that installed AME is serialized, the same is true in some cases, including Design Premium. In order to get the full range of format support, you must have one of the following installed: Premiere Pro, After Effects, Produciton Premium, or Master Collection.

Ah, I guess that potentially explains it. I know I've gotten a lot more experience since I last needed to use it, and I must just have not noticed it then. There doesn't seem to be anything that labels it as a trial or limited version though, and I have a couple of other programs that aren't "featured" on the box/website that were included. Does this mean that those would be limited or trial versions too?